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Crystal structure of aspergillus fumigatus GET3 with bound ADP

Analyse Crystal structure of aspergillus fumigatus GET3 with bound ADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3IBG
Type: protein
Length: 1,800 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ATPase, subunit of the get complex
EC: 3.6.3.16
UniProt: Q4WY07
Ligands: ADP
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 1 distinct chain · 45% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	ATPase, subunit of the get complex (EC 3.6.3.16)	protein	300	45% helix, 15% strand	Q4WY07

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 6 copies · chains A, F, B, C, D, E

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1154	0.85	0.86	122	ADP
2	1107	0.84	0.84	95	empty
3	1122	0.82	0.83	81	empty
4	533	0.71	0.80	52	ADP
5	472	0.69	0.80	37	ADP

Interfaces

12 interfaces between chains.

D–E · 1782 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 1778 Å² buried · 16 hydrogen bonds · protein-protein
A–F · 1744 Å² buried · 16 hydrogen bonds · protein-protein
E–F · 1430 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 1421 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

3IBG · Crystal structure of Aspergillus fumigatus Get3 with bound ADP · the same entry in another collection · chain D against D, TM-score 1.00
Q4WY07 · AlphaFold monomer V2.0 prediction for ATPase GET3 (Q4WY07) · a predicted model of the same protein · chain A against A, TM-score 0.91

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q4WY07
Elsewhere: RCSB PDB 3IBG · PDBe 3IBG · UniProt Q4WY07

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